Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024917.1 Corchorus olitorius cultivar O-4 contig24950, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 7332
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:1990 original size:28 final size:27

Alignment explanation


    Indices: 1958--2023  Score: 80
    Period size: 28  Copynumber: 2.4  Consensus size: 27

       1948 CAAAATTATT

                                         
       1958 GTTTTGCCCTTGGTCGACTAAAATTACCA
          1 GTTTTGCCCTTGGTCGACT-AAATTA-CA

                 *   *    *            
       1987 -TTTTACCCCTGGTTGACTAAATTACA
          1 GTTTTGCCCTTGGTCGACTAAATTACA

                       
       2013 GTTTTGCCCTT
          1 GTTTTGCCCTT

       2024 AAATGCCGGA


Statistics
Matches: 31,  Mismatches: 5, Indels: 4
        0.77            0.12        0.10

Matches are distributed among these distances:
  26    2  0.06
  27   14  0.45
  28   15  0.48

ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39


Consensus pattern (27 bp):   
GTTTTGCCCTTGGTCGACTAAATTACA

Found at i:5524 original size:12 final size:13

Alignment explanation


    Indices: 5496--5538  Score: 61
    Period size: 13  Copynumber: 3.4  Consensus size: 13

       5486 TCATGCACCC

                         
       5496 AAAATCATTTAAT
          1 AAAATCATTTAAT

                         
       5509 AAAATCATTT-AT
          1 AAAATCATTTAAT

                **       
       5521 AAAAAAATTTAAT
          1 AAAATCATTTAAT

                 
       5534 AAAAT
          1 AAAAT

       5539 AGTAATAAAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  12   10  0.38
  13   16  0.62

ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35


Consensus pattern (13 bp):   
AAAATCATTTAAT

Found at i:6611 original size:106 final size:104

Alignment explanation


    Indices: 6489--6696  Score: 371
    Period size: 106  Copynumber: 2.0  Consensus size: 104

       6479 GGCCACTACA

                                                                             
       6489 ACTGAAAATTTGCATTGGCTATATATATCCATGTGATTTTGGTTACTATGAACCATGCATGCGTC
          1 ACTGAAAATTTGCATTGGCTATATATATCCATGTGATTTTGGTTACTATGAACCATGCATGCGTC

                                                     
       6554 AAACACACACACACACACACAATATATATATATATATATAT
         66 -AA-ACACACACACACACACAATATATATATATATATATAT

                                                                         *   
       6595 ACTGAAAATTTGCATTGGCTATATATATCCATGTGATTTTGGTTACTATGAACCATGCATGTGTC
          1 ACTGAAAATTTGCATTGGCTATATATATCCATGTGATTTTGGTTACTATGAACCATGCATGCGTC

                   *          *                  
       6660 AAACACATACACACACACTATATATATATATATATAT
         66 AAACACACACACACACACAATATATATATATATATAT

       6697 GCTATTGAGA


Statistics
Matches: 99,  Mismatches: 3, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
 104   33  0.33
 105    2  0.02
 106   64  0.65

ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34


Consensus pattern (104 bp):   
ACTGAAAATTTGCATTGGCTATATATATCCATGTGATTTTGGTTACTATGAACCATGCATGCGTC
AAACACACACACACACACAATATATATATATATATATAT

Found at i:6749 original size:24 final size:22

Alignment explanation


    Indices: 6728--6786  Score: 82
    Period size: 22  Copynumber: 2.6  Consensus size: 22

       6718 GAATATATCA

                                    
       6728 ATACCATGTCTCAATAGCATATAT
          1 ATACCAT-TCTCAATA-CATATAT

               *                  
       6752 ATATCATTCTCAATACATATAT
          1 ATACCATTCTCAATACATATAT

               *         
       6774 ATATCATTCTCAA
          1 ATACCATTCTCAA

       6787 ATATCCAATT


Statistics
Matches: 34,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  22   20  0.59
  23    8  0.24
  24    6  0.18

ACGTcount: A:0.39, C:0.20, G:0.03, T:0.37


Consensus pattern (22 bp):   
ATACCATTCTCAATACATATAT

Found at i:6773 original size:22 final size:23

Alignment explanation


    Indices: 6736--6786  Score: 95
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       6726 CAATACCATG

                                   
       6736 TCTCAATAGCATATATATATCAT
          1 TCTCAATAGCATATATATATCAT

                                   
       6759 TCTCAATA-CATATATATATCAT
          1 TCTCAATAGCATATATATATCAT

                  
       6781 TCTCAA
          1 TCTCAA

       6787 ATATCCAATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  22   20  0.71
  23    8  0.29

ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39


Consensus pattern (23 bp):   
TCTCAATAGCATATATATATCAT
Done.